+Open data
-Basic information
Entry | Database: PDB / ID: 4uj5 | ||||||
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Title | Crystal structure of human Rab11-Rabin8-FIP3 | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / CILIARY TARGETING COMPLEX / CILIUM / VESICU TRANSPORT / MEMBRANE TRAFFICKING / RABIN8 / RAB11 / FIP3 | ||||||
Function / homology | Function and homology information Golgi to plasma membrane transport vesicle / protein localization to motile cilium / ciliary basal body-plasma membrane docking / regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of multivesicular body size / regulation of endocytic recycling / early endosome to recycling endosome transport / postsynaptic recycling endosome / establishment of protein localization to organelle ...Golgi to plasma membrane transport vesicle / protein localization to motile cilium / ciliary basal body-plasma membrane docking / regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of multivesicular body size / regulation of endocytic recycling / early endosome to recycling endosome transport / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization / protein localization to organelle / positive regulation of mitotic cytokinetic process / plasma membrane to endosome transport / regulation of cilium assembly / negative regulation of filopodium assembly / exosomal secretion / melanosome transport / amyloid-beta clearance by transcytosis / protein transmembrane transport / astral microtubule organization / proximal dendrite / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / BBSome-mediated cargo-targeting to cilium / regulation of vesicle-mediated transport / Golgi to plasma membrane transport / RAB geranylgeranylation / myosin V binding / Golgi to plasma membrane protein transport / positive regulation of cilium assembly / RAB GEFs exchange GTP for GDP on RABs / multivesicular body assembly / dynein light intermediate chain binding / protein localization to cilium / establishment of protein localization to membrane / protein localization to cell surface / TBC/RABGAPs / protein targeting to membrane / syntaxin binding / mitotic metaphase chromosome alignment / positive regulation of epithelial cell migration / exocytosis / cleavage furrow / centriolar satellite / mitotic spindle assembly / cilium assembly / vesicle-mediated transport / transport vesicle / Anchoring of the basal body to the plasma membrane / positive regulation of G2/M transition of mitotic cell cycle / centriole / phagocytic vesicle / multivesicular body / guanyl-nucleotide exchange factor activity / small monomeric GTPase / ciliary basal body / G protein activity / trans-Golgi network membrane / regulation of cytokinesis / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cytoplasmic vesicle membrane / trans-Golgi network / recycling endosome / spindle pole / Vasopressin regulates renal water homeostasis via Aquaporins / recycling endosome membrane / endocytic vesicle membrane / neuron projection development / protein transport / GTPase binding / lamellipodium / cytoplasmic vesicle / microtubule binding / vesicle / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / centrosome / glutamatergic synapse / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / protein-containing complex / extracellular exosome / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.604 Å | ||||||
Authors | Vetter, M. / Lorentzen, E. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2015 Title: Structure of Rab11-Fip3-Rabin8 Reveals Simultaneous Binding of Fip3 and Rabin8 Effectors to Rab11. Authors: Vetter, M. / Stehle, R. / Basquin, C. / Lorentzen, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uj5.cif.gz | 150.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uj5.ent.gz | 115.6 KB | Display | PDB format |
PDBx/mmJSON format | 4uj5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uj5_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4uj5_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4uj5_validation.xml.gz | 29.2 KB | Display | |
Data in CIF | 4uj5_validation.cif.gz | 39.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/4uj5 ftp://data.pdbj.org/pub/pdb/validation_reports/uj/4uj5 | HTTPS FTP |
-Related structure data
Related structure data | 4uj3C 4uj4C 1yzkS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 20844.451 Da / Num. of mol.: 2 / Fragment: GTPASE DOMAIN, RESIDUES 6-186 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62491 #2: Protein | Mass: 22217.479 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, RESIDUES 286-476 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96QF0 |
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-Non-polymers , 4 types, 164 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | Q70L POINT MUTATION |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow | pH: 7 Details: 0.1M HEPES PH 7.0, 0.2M LITHIUM SULFATE AND 24% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→50 Å / Num. obs: 24951 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 69.6 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.53→2.69 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1 / % possible all: 84 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YZK Resolution: 2.604→43.642 Å / SU ML: 0.49 / σ(F): 1.93 / Phase error: 34.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.604→43.642 Å
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Refine LS restraints |
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LS refinement shell |
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